{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T03:22:34Z","timestamp":1770434554538,"version":"3.49.0"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>\n              <jats:italic>Mycobacterium avium<\/jats:italic> subsp. <jats:italic>paratuberculosis<\/jats:italic> (Map) causes the chronic enteritis called paratuberculosis mainly in cattle, sheep and goats. Evidences that point out an association between Map and Crohn's Disease in humans are increasing. Strain differentiation among Map isolates has proved to be difficult and has limited the study of the molecular epidemiology of paratuberculosis. In order to asses the usefulness of the PCR based short sequence repeat (SSR) analysis of locus 1 and locus 8 in the epidemiological tracing of paratuberculosis strains we here compare for the first time the results of SSR and <jats:italic>Sna<\/jats:italic> BI-<jats:italic>Spe<\/jats:italic> I pulsed-field gel electrophoresis (PFGE) typing methods in a set of 268 Map isolates from different hosts (cattle, sheep, goats, bison, deer and wild boar).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>A total of nineteen different multi-locus SSR (SSR1_SSR8) types were identified amongst the 268 isolates compared to the 37 multiplex profiles differentiated by the <jats:italic>Sna<\/jats:italic> BI-<jats:italic>Spe<\/jats:italic> I PFGE. SSR type 7_4 was the predominant genotype (51.2% of all isolates and 54.3% of cattle isolates), but combined with PFGE results the abundance of the most prevalent genotype (7_4&amp;{2-1}) dropped down to 37.7%. SSR types 7_3 and 14_3 were significantly spread amongst isolates recovered from small ruminants. The comparison of SSR1_SSR8 and <jats:italic>Sna<\/jats:italic> BI-<jats:italic>Spe<\/jats:italic> I PFGE typing of these isolates has shown that both methods perform at similar discriminatory level. These were 0.691 and 0.693, respectively for SSR and PFGE as indicated Simpson's Index of Diversity, and 0.82 when calculated for combined SSR and PFGE genotypes. Overall, SSR1_SSR8 analysis seemed to detect higher levels of within-farm strain diversity and seemed to give higher year-related information. Combination of both typing methods revealed 20 multi-type farms out of the 33 bovine farms studied with more than one isolate.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The particular SSR and PFGE typing approaches described here are in general agreement but they showed some discrepancies that might reflect differing evolutionary processes of Map strains. Both methods are able to reciprocally complement their results and neither should be replaced with the other if sufficient material and time is available. Overall, the results of our comparative analyses suggest that, based on current methodologies available, a combined approach that includes SSR and PFGE seems to provide the highest level of discrimination for Map strain typing with meaningful epidemiological information.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2180-8-204","type":"journal-article","created":{"date-parts":[[2008,11,25]],"date-time":"2008-11-25T19:13:10Z","timestamp":1227640390000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Comparative analysis of Mycobacterium avium subsp. paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel electrophoresis typing"],"prefix":"10.1186","volume":"8","author":[{"given":"Iker","family":"Sevilla","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingling","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alongkorn","family":"Amonsin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseba M","family":"Garrido","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria V","family":"Geijo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vivek","family":"Kapur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ram\u00f3n A","family":"Juste","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,11,25]]},"reference":[{"key":"637_CR1","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1097\/MOG.0b013e3282f1dcc4","volume":"24","author":"MA Behr","year":"2008","unstructured":"Behr MA, Kapur V: The evidence for Mycobacterium paratuberculosis in Crohn's disease. Curr Opin Gastroenterol. 2008, 24: 17-21.","journal-title":"Curr Opin Gastroenterol"},{"key":"637_CR2","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/S1473-3099(03)00724-2","volume":"3","author":"RJ Greenstein","year":"2003","unstructured":"Greenstein RJ: Is Crohn's disease caused by a mycobacterium? Comparisons with leprosy, tuberculosis, and Johne's disease. Lancet Infect Dis. 2003, 3: 507-514. 10.1016\/S1473-3099(03)00724-2.","journal-title":"Lancet Infect Dis"},{"key":"637_CR3","doi-asserted-by":"publisher","first-page":"e2537","DOI":"10.1371\/journal.pone.0002537","volume":"3","author":"RA Juste","year":"2008","unstructured":"Juste RA, Elguezabal N, Garrido JM, Pavon A, Geijo MV, Sevilla I, Cabriada JL, Tejada A, Garc\u00eda-Campos F, Casado R, et al.: On the prevalence of M. avium subspecies paratuberculosis DNA in the blood of healthy individuals and patients with inflammatory bowel disease. PLoS ONE. 2008, 3: e2537-10.1371\/journal.pone.0002537.","journal-title":"PLoS ONE"},{"key":"637_CR4","volume-title":"Int J Infect Dis","author":"RA Juste","year":"2008","unstructured":"Juste RA, Elguezabal N, Pav\u00f3n A, Garrido JM, Geijo MV, Sevilla I, Cabriada JL, Tejada A, Garc\u00eda-Campos F, Casado R, et al.: Association between Mycobacterium avium subsp. paratuberculosis DNA in blood and cellular and humoral immune response in Inflammatory Bowel Disease patients and controls. Int J Infect Dis. 2008,"},{"issue":"1","key":"637_CR5","doi-asserted-by":"crossref","first-page":"151","DOI":"10.20506\/rst.20.1.1274","volume":"20","author":"DJ Kennedy","year":"2001","unstructured":"Kennedy DJ, Benedictus G: Control of Mycobacterium avium subsp. paratuberculosis infection in agricultural species. Rev Sci Tech. 2001, 20 (1): 151-179.","journal-title":"Rev Sci Tech"},{"key":"637_CR6","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1111\/j.1751-0813.2001.tb11980.x","volume":"79","author":"RJ Whittington","year":"2001","unstructured":"Whittington RJ, Sergeant ES: Progress towards understanding the spread, detection and control of Mycobacterium avium subsp. paratuberculosis in animal populations. Aust Vet J. 2001, 79: 267-278. 10.1111\/j.1751-0813.2001.tb11980.x.","journal-title":"Aust Vet J"},{"key":"637_CR7","doi-asserted-by":"crossref","first-page":"966","DOI":"10.4315\/0362-028X-68.5.966","volume":"68","author":"JL Ellingson","year":"2005","unstructured":"Ellingson JL, Anderson JL, Koziczkowski JJ, Radcliff RP, Sloan SJ, Allen SE, Sullivan NM: Detection of viable Mycobacterium avium subsp. paratuberculosis in retail pasteurized whole milk by two culture methods and PCR. J Food Prot. 2005, 68: 966-972.","journal-title":"J Food Prot"},{"key":"637_CR8","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1111\/j.1365-2672.2005.02598.x","volume":"98","author":"IR Grant","year":"2005","unstructured":"Grant IR: Zoonotic potential of Mycobacterium avium ssp. paratuberculosis: the current position. J Appl Microbiol. 2005, 98: 1282-1293. 10.1111\/j.1365-2672.2005.02598.x.","journal-title":"J Appl Microbiol"},{"key":"637_CR9","doi-asserted-by":"crossref","first-page":"327","DOI":"10.17221\/5631-VETMED","volume":"50","author":"K Hruska","year":"2005","unstructured":"Hruska K, Bartos M, Kralik P, Pavlik I: Mycobacterium avium subsp. paratuberculosis in powdered infant milk: paratuberculosis in cattle: the public health problem to be solved. Vet Med (Praha). 2005, 50: 327-335.","journal-title":"Vet Med (Praha)"},{"key":"637_CR10","doi-asserted-by":"publisher","first-page":"8934","DOI":"10.1128\/AEM.71.12.8934-8936.2005","volume":"71","author":"J Ikonomopoulos","year":"2005","unstructured":"Ikonomopoulos J, Pavlik I, Bartos M, Svastova P, Ayele WY, Roubal P, Lukas J, Cook N, Gazouli M: Detection of Mycobacterium avium subsp. paratuberculosis in retail cheeses from Greece and the Czech Republic. Appl Environ Microbiol. 2005, 71: 8934-8936. 10.1128\/AEM.71.12.8934-8936.2005.","journal-title":"Appl Environ Microbiol"},{"key":"637_CR11","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1016\/j.micinf.2005.12.003","volume":"8","author":"AS Motiwala","year":"2006","unstructured":"Motiwala AS, Li L, Kapur V, Sreevatsan S: Current understanding of the genetic diversity of Mycobacterium avium subsp. paratuberculosis. Microbes Infect. 2006, 8: 1406-1418. 10.1016\/j.micinf.2005.12.003.","journal-title":"Microbes Infect"},{"key":"637_CR12","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/1471-2180-7-18","volume":"7","author":"I Sevilla","year":"2007","unstructured":"Sevilla I, Garrido JM, Geijo M, Juste RA: Pulsed-field gel electrophoresis profile homogeneity of Mycobacterium avium subsp. paratuberculosis isolates from cattle and heterogeneity of those from sheep and goats. BMC Microbiol. 2007, 7: 18-10.1186\/1471-2180-7-18.","journal-title":"BMC Microbiol"},{"key":"637_CR13","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1128\/JCM.42.4.1694-1702.2004","volume":"42","author":"A Amonsin","year":"2004","unstructured":"Amonsin A, Li LL, Zhang Q, Bannantine JP, Motiwala AS, Sreevatsan S, Kapur V: Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp. paratuberculosis strains. J Clin Microbiol. 2004, 42: 1694-1702. 10.1128\/JCM.42.4.1694-1702.2004.","journal-title":"J Clin Microbiol"},{"key":"637_CR14","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1111\/j.1751-0813.2000.tb10590.x","volume":"78","author":"DV Cousins","year":"2000","unstructured":"Cousins DV, Williams SN, Hope A, Eamens GJ: DNA fingerprinting of Australian isolates of Mycobacterium avium subsp. paratuberculosis using IS 900 RFLP. Aust Vet J. 2000, 78: 184-190. 10.1111\/j.1751-0813.2000.tb10590.x.","journal-title":"Aust Vet J"},{"key":"637_CR15","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1751-0147-46-13","volume":"46","author":"B Djonne","year":"2005","unstructured":"Djonne B, Pavlik I, Svastova P, Bartos M, Holstad G: IS 900 restriction fragment length polymorphism (RFLP) analysis of Mycobacterium avium subsp. paratuberculosis isolates from goats and cattle in Norway. Acta Vet Scand. 2005, 46: 13-18. 10.1186\/1751-0147-46-13.","journal-title":"Acta Vet Scand"},{"key":"637_CR16","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1111\/j.1751-0813.1997.tb11259.x","volume":"75","author":"MM Feizabadi","year":"1997","unstructured":"Feizabadi MM, Robertson ID, Hope A, Cousins DV, Hampson DJ: Differentiation of Australian isolates of Mycobacterium paratuberculosis using pulsed-field gel electrophoresis. Aust Vet J. 1997, 75: 887-889. 10.1111\/j.1751-0813.1997.tb11259.x.","journal-title":"Aust Vet J"},{"key":"637_CR17","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.1128\/JCM.41.5.2015-2026.2003","volume":"41","author":"AS Motiwala","year":"2003","unstructured":"Motiwala AS, Strother M, Amonsin A, Byrum B, Naser SA, Stabel JR, Shulaw WP, Bannantine JP, Kapur V, Sreevatsan S: Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: evidence for limited strain diversity, strain sharing, and identification of unique targets for diagnosis. J Clin Microbiol. 2003, 41: 2015-2026. 10.1128\/JCM.41.5.2015-2026.2003.","journal-title":"J Clin Microbiol"},{"key":"637_CR18","doi-asserted-by":"publisher","first-page":"5345","DOI":"10.1128\/JCM.42.11.5345-5348.2004","volume":"42","author":"AH Ghadiali","year":"2004","unstructured":"Ghadiali AH, Strother M, Naser SA, Manning EJ, Sreevatsan S: Mycobacterium avium subsp. paratuberculosis strains isolated from Crohn's disease patients and animal species exhibit similar polymorphic locus patterns. J Clin Microbiol. 2004, 42: 5345-5348. 10.1128\/JCM.42.11.5345-5348.2004.","journal-title":"J Clin Microbiol"},{"key":"637_CR19","doi-asserted-by":"publisher","first-page":"2111","DOI":"10.1128\/JCM.43.5.2111-2117.2005","volume":"43","author":"AS Motiwala","year":"2005","unstructured":"Motiwala AS, Strother M, Theus NE, Stich RW, Byrum B, Shulaw WP, Kapur V, Sreevatsan S: Rapid detection and typing of strains of Mycobacterium avium subsp. paratuberculosis from broth cultures. J Clin Microbiol. 2005, 43: 2111-2117. 10.1128\/JCM.43.5.2111-2117.2005.","journal-title":"J Clin Microbiol"},{"key":"637_CR20","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1128\/jcm.34.7.1617-1621.1996","volume":"34","author":"R Bauerfeind","year":"1996","unstructured":"Bauerfeind R, Benazzi S, Weiss R, Schliesser T, Willems H, Baljer G: Molecular characterization of Mycobacterium paratuberculosis isolates from sheep, goats and cattle by hybridization with a DNA probe to insertion element IS 900. J Clin Microbiol. 1996, 34: 1617-1621.","journal-title":"J Clin Microbiol"},{"key":"637_CR21","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1128\/jcm.28.7.1591-1596.1990","volume":"28","author":"DM Collins","year":"1990","unstructured":"Collins DM, Gabric DM, de Lisle GW: Identification of two groups of Mycobacterium paratuberculosis strains by restriction analysis and DNA hybridization. J Clin Microbiol. 1990, 28: 1591-1596.","journal-title":"J Clin Microbiol"},{"key":"637_CR22","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.vetmic.2006.01.008","volume":"115","author":"L de Juan","year":"2006","unstructured":"de Juan L, Alvarez J, Aranaz A, Rodriguez A, Romero B, Bezos J, Mateos A, Dominguez L: Molecular epidemiology of Types I\/III strains of Mycobacterium avium subspecies paratuberculosis isolated from goats and cattle. Vet Microbiol. 2006, 115: 102-110. 10.1016\/j.vetmic.2006.01.008.","journal-title":"Vet Microbiol"},{"key":"637_CR23","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/S0167-7012(99)00091-3","volume":"38","author":"I Pavlik","year":"1999","unstructured":"Pavlik I, Horvathova A, Dvorska L, Bartl J, Svastova P, du Maine R, Rychlik I: Standardisation of restriction fragment length polymorphism analysis for Mycobacterium avium subspecies paratuberculosis. J Microbiol Methods. 1999, 38: 155-167. 10.1016\/S0167-7012(99)00091-3.","journal-title":"J Microbiol Methods"},{"key":"637_CR24","doi-asserted-by":"publisher","first-page":"1798","DOI":"10.1128\/JCM.40.5.1798-1804.2002","volume":"40","author":"K Stevenson","year":"2002","unstructured":"Stevenson K, Hughes VM, de Juan L, Inglis NF, Wright F, Sharp JM: Molecular characterization of pigmented and nonpigmented isolates of Mycobacterium avium subsp. paratuberculosis. J Clin Microbiol. 2002, 40: 1798-1804. 10.1128\/JCM.40.5.1798-1804.2002.","journal-title":"J Clin Microbiol"},{"key":"637_CR25","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.1128\/JCM.38.9.3240-3248.2000","volume":"38","author":"RJ Whittington","year":"2000","unstructured":"Whittington RJ, Hope AF, Marshall DJ, Taragel CA, Marsh I: Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: IS 900 restriction fragment length polymorphism and IS 1311 polymorphism analyses of isolates from animals and a human in Australia. J Clin Microbiol. 2000, 38: 3240-3248.","journal-title":"J Clin Microbiol"},{"key":"637_CR26","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.20506\/rst.24.3.1634","volume":"24","author":"I Sevilla","year":"2005","unstructured":"Sevilla I, Singh SV, Garrido JM, Aduriz G, Rodr\u00edguez S, Geijo MV, Whittington RJ, Saunders V, Whitlock RH, Juste RA: PCR-REA genotype of paratuberculosis strains isolated from different host species and geographic locations. Rev \u2013 Off Int Epizoot. 2005, 24: 1061-1066.","journal-title":"Rev \u2013 Off Int Epizoot"},{"key":"637_CR27","doi-asserted-by":"publisher","first-page":"972","DOI":"10.1128\/JCM.01801-07","volume":"46","author":"P Mobius","year":"2008","unstructured":"Mobius P, Luyven G, Hotzel H, Kohler H: High genetic diversity among Mycobacterium avium subsp. paratuberculosis strains from German cattle herds shown by combination of IS900 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing. J Clin Microbiol. 2008, 46: 972-981. 10.1128\/JCM.01801-07.","journal-title":"J Clin Microbiol"},{"key":"637_CR28","doi-asserted-by":"publisher","first-page":"2404","DOI":"10.1128\/JCM.00476-07","volume":"45","author":"VC Thibault","year":"2007","unstructured":"Thibault VC, Grayon M, Boschiroli ML, Hubbans C, Overduin P, Stevenson K, Gutierrez MC, Supply P, Biet F: New variable-number tandem-repeat markers for typing Mycobacterium avium subsp. paratuberculosis and M. avium strains: comparison with IS900 and IS1245 restriction fragment length polymorphism typing. J Clin Microbiol. 2007, 45: 2404-2410. 10.1128\/JCM.00476-07.","journal-title":"J Clin Microbiol"},{"key":"637_CR29","doi-asserted-by":"publisher","first-page":"1703","DOI":"10.1128\/JCM.42.4.1703-1712.2004","volume":"42","author":"AS Motiwala","year":"2004","unstructured":"Motiwala AS, Amonsin A, Strother M, Manning EJ, Kapur V, Sreevatsan S: Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolates recovered from wild animal species. J Clin Microbiol. 2004, 42: 1703-1712. 10.1128\/JCM.42.4.1703-1712.2004.","journal-title":"J Clin Microbiol"},{"key":"637_CR30","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1006\/mcpr.1998.0194","volume":"12","author":"R Whittington","year":"1999","unstructured":"Whittington R, Marsh I, Choy E, Cousins D: Polymorphism in IS 1311, an insertion sequence common to Mycobacterium avium and Mycobacterium avium subsp. paratuberculosis, can be used to distinguish between and within these species. Mol Cell Probes. 1999, 12: 349-358. 10.1006\/mcpr.1998.0194.","journal-title":"Mol Cell Probes"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2180-8-204.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T10:10:45Z","timestamp":1630491045000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/1471-2180-8-204"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,11,25]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["637"],"URL":"https:\/\/doi.org\/10.1186\/1471-2180-8-204","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,11,25]]},"assertion":[{"value":"11 July 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"204"}}